PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Cc11_g10560
Common NameGSCOC_T00032561001
Organism
Coffea canephora
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Gentianales; Rubiaceae; Ixoroideae; Coffeeae; Coffea
Family RAV
Protein Properties Length: 379aa    MW: 41657.1 Da    PI: 9.662
Description RAV family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cc11_g10560genomeCGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP243.48.2e-1471119155
          AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                  s++kGV   + +grW A+I++      ++r++lg+f  +eeAa+a++ a+++++g
  Cc11_g10560  71 SRFKGVVPQP-NGRWGAQIYEK-----HQRVWLGTFNEEEEAARAYDIAAQRFRG 119
                  689***9788.8*********3.....5*************************98 PP
2B3103.31.4e-32202304199
                  EEEE-..-HHHHTT-EE--HHH.HTT....---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EE CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh....ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvv 94 
                  f+k+ tpsdv+k++rlv+pk++ae+h    +g++ +++ l +ed  g++W+++++y+++s++yvltkGW++Fvk+++Lk+gD+v F+++   +++l++
  Cc11_g10560 202 FEKAVTPSDVGKLNRLVIPKQHAEKHfplqSGNTSKGVLLNFEDMGGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLKAGDIVSFQRSTGADKQLYI 299
                  89****************************88999****************************************************88668888899 PP

                  EEE-S CS
           B3  95 kvfrk 99 
                   + r+
  Cc11_g10560 300 DWKRR 304
                  88876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF008479.8E-971119IPR001471AP2/ERF domain
CDDcd000183.00E-2671126No hitNo description
SuperFamilySSF541712.75E-1771127IPR016177DNA-binding domain
PROSITE profilePS5103220.25772127IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.102.5E-2072127IPR001471AP2/ERF domain
SMARTSM003801.2E-3072133IPR001471AP2/ERF domain
Gene3DG3DSA:2.40.330.101.3E-41196306IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.31E-30200304IPR015300DNA-binding pseudobarrel domain
CDDcd100173.47E-29201290No hitNo description
PfamPF023626.1E-30202304IPR003340B3 DNA binding domain
PROSITE profilePS5086314.889202305IPR003340B3 DNA binding domain
SMARTSM010193.5E-25202305IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0048573Biological Processphotoperiodism, flowering
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 379 aa     Download sequence    Send to blast
MDNSSIDEST TSDNSFASSA APASLSNMSL PVNIKSSPEQ QSLCRVGSGA SSMIIDAEVG  60
VEAESRKLPS SRFKGVVPQP NGRWGAQIYE KHQRVWLGTF NEEEEAARAY DIAAQRFRGR  120
DAVTNFKPLN EAEEDDVEAA FLSCHSKAEI VDMLRKHTYN DELEQSKRNY GLDGNGKKGC  180
KGIAGLHSFG YQKTTKAREQ LFEKAVTPSD VGKLNRLVIP KQHAEKHFPL QSGNTSKGVL  240
LNFEDMGGKV WRFRYSYWNS SQSYVLTKGW SRFVKEKNLK AGDIVSFQRS TGADKQLYID  300
WKRRNGAAEA APPVAAGISI PIQPVQMVRL FGVNIFKVPL PVNGVVMDSN SSCSGKRVRG  360
MELLGLECSK KPRAIGAL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1wid_A2e-6019930711120DNA-binding protein RAV1
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional repressor of flowering time on long day plants. Acts directly on FT expression by binding 5'-CAACA-3' and 5'-CACCTG-3 sequences. Functionally redundant with TEM2. {ECO:0000269|PubMed:18718758}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00024PBMTransfer from AT1G25560Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Expressed with a circadian rhythm showing a peak at dawn. {ECO:0000269|PubMed:18718758}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_027097064.10.0AP2/ERF and B3 domain-containing transcription factor RAV1-like
SwissprotQ9C6M51e-145RAVL1_ARATH; AP2/ERF and B3 domain-containing transcription repressor TEM1
TrEMBLA0A068TYZ80.0A0A068TYZ8_COFCA; Uncharacterized protein
STRINGVIT_01s0011g03070.t010.0(Vitis vinifera)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA29582453
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G25560.11e-145RAV family protein
Publications ? help Back to Top
  1. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  2. Choi D, et al.
    iNID: an analytical framework for identifying network models for interplays among developmental signaling in Arabidopsis.
    Mol Plant, 2014. 7(5): p. 792-813
    [PMID:24380880]
  3. Sgamma T,Jackson A,Muleo R,Thomas B,Massiah A
    TEMPRANILLO is a regulator of juvenility in plants.
    Sci Rep, 2014. 4: p. 3704
    [PMID:24424565]
  4. Matías-Hernández L,Aguilar-Jaramillo AE,Marín-González E,Suárez-López P,Pelaz S
    RAV genes: regulation of floral induction and beyond.
    Ann. Bot., 2014. 114(7): p. 1459-70
    [PMID:24812253]
  5. Marín-González E, et al.
    SHORT VEGETATIVE PHASE Up-Regulates TEMPRANILLO2 Floral Repressor at Low Ambient Temperatures.
    Plant Physiol., 2015. 169(2): p. 1214-24
    [PMID:26243615]
  6. Matías-Hernández L, et al.
    TEMPRANILLO Reveals the Mesophyll as Crucial for Epidermal Trichome Formation.
    Plant Physiol., 2016. 170(3): p. 1624-39
    [PMID:26802039]